The atomic force microscope (AFM) is becoming increasingly useful for studying ultra-structure and functional properties of biological molecules and tissue. The DBEPS Instrumentation Research and Development Resource is strengthening the AFM capabilities at NIH to support the diverse needs of IC scientific projects, in particular, adapting the AFM platform to allow measurement of biological samples. Using DBEPS expertise in optics, electronics, mechanical design, microfluidics, and other areas, associated instrumentation and quantitative analysis methods are being pursued to advance AFM technology and apply it to solve novel biomedical problems. New AFM components are being acquired and integrated to expand our facility capabilities towards meeting the varying needs of intramural researchers from across NIH. Collaborative intramural biological projects include the investigation of the viscoelastic energetics of the protein clathrin and its assemblies that are important to subcellular protein trafficking (NICHD), structure studies of an Escherichia coli derived Plasmodium falciparum Merozoite Surface Protein 3 as a potential human malaria vaccine component (NIAID), organization of rhodopsin on the surface of native disk membranes (NIAAA), surface modified protein interaction dynamics (NIDDK), DNA-protein interactions in gene regulation pathways (NCI), cytochrome c adsorption to anionic supported bilayers (NIDDK), and measured mechanical properties of the tectorial membrane in the mammalian cochlea (NIDCD). [unreadable] [unreadable] A strong focus of our AFM technology development is to combine optical spectroscopies with AFM for multimodal ultra-sensitive nanometric sample characterizations. In particular, total internal reflection fluorescent microscopy (TIRFM) and confocal Raman microscopy are combined with suitable AFM instruments to observe and correlate multiple structural properties. Sensitive detection devices, configurations, and vibration-isolation setups are being incorporated toward achieving single biomolecule resolution and sensitivity. We are optimizing our instrumentations through studies of quantum dots (q-dots), which are nanocrystals with revolutionary fluorescence performance and huge potential in nanotechnology and related fields. As q-dots interact with their environment, our TIRFM-AFM and Raman-AFM are used to observe their nanocrystal cores and biocompatible coatings. We aim to understand the single particle behavior by correlating high resolution topological, mechanical, and electrostatic profiles with optical properties such as fluorescent spectra, intermittency (i.e. blinking), and photostability. [unreadable] [unreadable] Other examples of technology development for enhancing the AFM capabilities include the use of elastomeric microchannels to temporarily create a microdevice on an AFM substrate. Because flow in such microchannels is laminar, all mixing is diffusive, which allows us to create a well-controlled buffer gradient, either in ionic strength or pH, over a distance of a few hundred microns. This permits rapid sampling of buffer conditions for sample deposition on AFM substrates and offers the potential of reducing substantially the time required to optimize adsorption conditions for AFM imaging. Previously, a temperature controlled environmental chamber has also been developed to allow samples that exhibit temperature dependent properties to be examined. The chamber is capable of 0.1 degree stability within a temperature range from 10 to 40 degrees Celsius. A perfusion chamber has been developed to enable a single cell to be retained for examination and permitting manipulation of the extra-cellular environment.[unreadable] [unreadable] One example of our AFM applications is to the study of the mechanical properties associated with vesicle formation and vesicular trafficking. In this particular project we examine the assembly of clathrin triskelions into polyhedral coats of about 100-nanometer diameter that is believed to play a central role in receptor-mediated endocytosis and intracellular trafficking from the trans-Golgi network. Knowledge of the mechanical properties of the clathrin coat is needed in order to fully understand the function of the coat in the dynamical control of vesicle formation. To unravel the intricacy of their molecular constructs, we examine the mechanical properties of CCVs while developing new schemes of atomic force microscopy (AFM) and related analyses. By focusing on CCV deformation in quantitative response to varying AFM-substrate compression force, we have estimated that the bending rigidity of the CCV composite shell is 285 +/- 30 kBT, which is about 20 times that of either the outer clathrin cage or inner vesicle membrane. This result indicates a flexible coupling between the clathrin coat and the inner membrane that can be up or down regulated, potentially by orders of magnitude, during the vesicular trafficking in cells.